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a3fe

Automated Adaptive Absolute alchemical Free Energy calculator

abfeconv

protocols for adaptive sampling of absolute binding free energy cals

ack1_data

This repository contains scripts and relevant data used for the analysis of the ACK_1 dataset using alchemical free energy methods.

afe_network_gen

Project repository for generating statistically optimal perturbation network using machine-learned perturbation difficulties.

amberfepcyclophilins

Masters Project for RBFE calculations for cyclophilins

amd-md-msm_analysis

Set of Scripts used to analyse data and produce some of the results in Juarez-Jimenez et.al. Chem. Sci. 2020, 11, 2670

ammo

benchmark

A selection of scripts to run Sire and openMM benchmarks on the same datasets

bgflow

Boltzmann Generators and Normalizing Flows in PyTorch

bgflowexperiments

Experiments with Boltzmann Generators

biomolsetuppaper

biosimspace

Code and resources for the EPSRC BioSimSpace project.

biosimspace_examples

biosimspace_tutorial

biosimspacecloud

Files used to put BioSimSpace onto the cloud (via Fn functions)

biosimspacetutorials

biosimspacewebsite

Files needed to configure the BioSimSpace website and associated Jupyter notebooks on Kubernetes

brahan_utilities

bss_fep_advanced_tut_bg

example workflow of FEP using BSS

bssccpbiosim2022

Material for the BioSimSpace workshop at the upcoming 2022 CCPBioSim Training Week

bssopenffhack

Exploring interoperability of BioSimSpace and OpenFF toolkits

ccgbsa

Simulations of coiled coils with OpenMM

ccp-biosim-workshop

chargingcorrections

Scripts and protocols for charging free energies correction project

cluster

This repository is used for tracking any issues regarding the cluster

cov2-s-pep

Datasets, code and docs related to the SARS-CoV-2-S peptide project

custom_residus_parametrization

cutoff-corrections

Set of Sire scripts to correct free energy changes for finite size errors in electrostatic and dispersion interactions

cyp-trivector

cypacatalysis_input